Chromatin Organization in Glioma Initiation

神经胶质瘤起始中的染色质组织

• 批准号: 10156402
• 负责人: Devin Michael Bready
• 金额: $ 3.78万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-07 至 2024-01-06
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10156402
• 关键词: 3-Dimensional; ATAC-seq; ATRX gene; Address; Adjuvant; Architecture; Astrocytoma; Binding; Biological Assay; Brain; CCCTC-binding factor; CRISPR interference; Cell Cycle; Cell Survival; Cell model; Cells; Characteristics; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; DNA; Data; Development; Dioxygenases; Distal; Distal Enhancer Elements; Engineering; Enhancers; Environment; Enzyme Inhibition; Enzymes; Epigenetic Process; Event; Excision; Family; Fellowship; Functional disorder; Genes; Genetic; Genetic Enhancer Element; Genetic Transcription; Genome; Genomics; Glioblastoma; Glioma; Gliomagenesis; Guide RNA; Histones; Human; Hypermethylation; Impairment; Incidence; Indolent; Intergenic DNA; Isocitrate Dehydrogenase; Lead; Light; Location; Maintenance; Malignant - descriptor; Malignant Neoplasms; Mediating; Metabolism; Modeling; Molecular Conformation; Mutation; Nuclear; Oncogenic; Operative Surgical Procedures; Other Genetics; Pathway interactions; Patients; Pattern; Phenotype; Primary Brain Neoplasms; Production; Publishing; Radiation; Regulation; Reporter; Role; Secondary to; Specimen; TP53 gene; Testing; Transcript; Tumor Suppressor Genes; Tumor Suppressor Proteins; Undifferentiated; Work; XCL1 gene; alpha ketoglutarate; base; cell type; chemotherapeutic agent; epigenome; gain of function mutation; gene interaction; genomic locus; histone demethylase; inhibitor/antagonist; insight; knock-down; mutant; neoplastic cell; nerve stem cell; neurodevelopment; neuroregulation; novel; prevent; promoter; recruit; restoration; sex; small hairpin RNA; stem cell differentiation; stem cell model; transcription factor; transcriptome; transcriptome sequencing; transcriptomics; translocase; treatment strategy; tumor; tumorigenesis; young adult

Project Summary Glioma is the most common primary brain tumor and represents a disproportionate percentage of cancer fatalities in relation to its incidence. In the last decade, it has been discovered that nearly all lower grade gliomas harbor a characteristic gain of function mutation in Isocitrate dehydrogenase I (IDH1) allowing the enzyme to form a novel oncometabolite. These lower grade gliomas invariably progress to high-grade, aggressive glioblastoma. At neither the low-grade nor high-grade stage are directed therapies available and current treatment is limited to surgical resection and adjuvant radiation and alkylating chemotherapeutic agents. Recent efforts have attempted to employ inhibitors of mutant IDH1 to treat these tumors but early evidence is mixed, indicating that mutant IDH1 induces long-lasting epigenetic changes that do not dissipate upon inhibition of the oncometabolite’s production. Studying these tumors has proven difficult compared to IDH wildtype glioma as patient tumors cannot be readily grown in culture. To address this, our group generated a model of low-grade glioma in human neural stem cells (NSCs) which are strongly implicated as the cell of origin for these tumors. This model, referred to as 3- Hit NSCs, reaffirmed previous observations that the IDH1 mutant induces a block to neural precursor differentiation. Strikingly, it revealed that this block to differentiation in NSCs can be completely rescued by restoration of expression of the transcription factor (sex determining region Y)-box 2 (SOX2). Moreover, this reduction of expression and the associated differentiation phenotype occurs secondary to profound changes in 3-dimensional chromatin organization around the SOX2 genomic locus. The proposed work in this fellowship will examine how central these changes in chromatin organization are to the glioma-phenotype in NSCs and will characterize the SOX2 enhancer environment in NSCs to understand its regulation in glioma initiation. Preliminary data suggests that disruption of the SOX2 TAD by preventing binding of the genome organizer CTCF mirrors reduction in SOX2 expression seen in 3-Hit NSCs. Additionally, those regions which lose interaction with the SOX2 promoter in 3-Hit NSCs correlate with regions found to have marks of being active enhancers in other SOX2 expressing cell types. We hypothesize that CTCF eviction in 3-Hit NSCs results in a loss of SOX2 expression through a disruption of promoter interactions with previously uncharacterized enhancers in the SOX2 locus. To evaluate this hypothesis, I will employ complementary and independent approaches that address the involvement of CTCF mediated chromatin architecture dysfunction in glioma initiation, identify novel SOX2 enhancers in NSCs, examine the activity of these enhancers in glioma initiation, and dissect the activity of these enhancers in stem cell differentiation. Finally, I will validate the relevance of these enhancers in glioma by inferring their activity from single cell ATAC-sequencing of surgical low-grade glioma specimens. Through these approaches, paired with the support of the Placantonakis and Skok labs, I will characterize the role of chromatin disorganization in glioma initiation and help understand the developmental and oncogenic regulation of SOX2.

项目概要 神经胶质瘤是最常见的原发性脑肿瘤，占癌症死亡人数的不成比例。 其发生率。在过去的十年中，人们发现几乎所有低级别神经胶质瘤都具有特征增益 异柠檬酸脱氢酶 I (IDH1) 的功能突变使该酶形成一种新的致癌代谢物。这些较低 级别胶质瘤总是进展为高级、侵袭性胶质母细胞瘤。无论是低品还是高品阶段都没有 可用的定向疗法，目前的治疗仅限于手术切除和辅助放射和烷化 化疗剂。最近的努力尝试使用突变 IDH1 抑制剂来治疗这些肿瘤，但早期 证据不一，表明突变 IDH1 会诱导持久的表观遗传变化，且这种变化在抑制后不会消失 致癌代谢物的产生。与 IDH 野生型神经胶质瘤相比，研究这些肿瘤已被证明是困难的 肿瘤不易在培养物中生长。为了解决这个问题，我们的小组在人类中建立了低级别神经胶质瘤模型 神经干细胞（NSC）与这些肿瘤的起源细胞密切相关。该模型称为 3- 打击 NSC，重申了之前的观察结果，即 IDH1 突变体会​​诱导神经前体分化受阻。 引人注目的是，它揭示了这种对 NSC 分化的阻碍可以通过恢复 转录因子（性别决定区 Y）-框 2 (SOX2)。此外，这种表达的减少和相关的 分化表型继发于 SOX2 周围 3 维染色质组织的深刻变化 基因组位点。该奖学金的拟议工作将研究染色质组织中这些变化的重要性 神经干细胞中的神经胶质瘤表型，并将表征 NSC 中的 SOX2 增强子环境以了解其调节 在神经胶质瘤起始过程中。初步数据表明，通过阻止基因组结合来破坏 SOX2 TAD 组织者 CTCF 反映了 3-Hit NSC 中 SOX2 表达的减少。此外，那些失去的地区 3-Hit NSC 中与 SOX2 启动子的相互作用与发现具有活性增强子标记的区域相关 其他表达 SOX2 的细胞类型。我们假设 3-Hit NSC 中的 CTCF 驱逐导致 SOX2 表达丧失 通过破坏启动子与 SOX2 基因座中先前未表征的增强子的相互作用。评估 在这个假设中，我将采用补充和独立的方法来解决 CTCF 介导的参与问题 神经胶质瘤起始过程中染色质结构功能障碍，识别 NSC 中新型 SOX2 增强子，检查 这些增强子在神经胶质瘤起始中的作用，并剖析这些增强子在干细胞分化中的活性。最后，我会 通过从手术的单细胞 ATAC 测序推断这些增强子的活性，验证这些增强子在神经胶质瘤中的相关性 低级别神经胶质瘤标本。通过这些方法，再加上 Placantonakis 和 Skok 实验室的支持，我将 表征染色质解体在神经胶质瘤发生中的作用，并帮助了解发育和致癌性 SOX2 的监管。